Multiple functions of flagellar motility and chemotaxis in bacterial physiology

FEMS Microbiology Reviews, Год журнала: 2021, Номер 45(6)

Опубликована: Июль 2, 2021

Most swimming bacteria are capable of following gradients nutrients, signaling molecules and other environmental factors that affect bacterial physiology. This tactic behavior became one the most-studied model systems for signal transduction quantitative biology, underlying molecular mechanisms well characterized in Escherichia coli several bacteria. In this review, we focus primarily on less understood aspect chemotaxis, namely its physiological relevance individual cells populations. As evident from multiple recent studies, even same species flagellar motility chemotaxis might serve roles, depending conditions. Among these, finding sources nutrients more generally locating niches optimal growth appear to be major functions which could explain many chemoeffector preferences as gene regulation. Chemotaxis also enhance efficiency colonization by motile bacteria, involves intricate interplay between collective behaviors trade-offs motility. Finally, play roles including swarming, biofilm formation autoaggregation, their interactions with animal plant hosts.

Язык: Английский

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The ecological roles of bacterial chemotaxis

Nature Reviews Microbiology, Год журнала: 2022, Номер 20(8), С. 491 - 504

Опубликована: Март 15, 2022

Язык: Английский

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Chemotaxis as a navigation strategy to boost range expansion

Nature, Год журнала: 2019, Номер 575(7784), С. 658 - 663

Опубликована: Ноя. 6, 2019

Язык: Английский

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A Simple Three-Dimensional Microfluidic Platform for Studying Chemotaxis and Cell Sorting

Lab on a Chip, Год журнала: 2025, Номер unknown

Опубликована: Янв. 1, 2025

Microbial chemotaxis plays a key role in diversity of biological and ecological processes. Although microfluidics-based assays have been applied to investigate bacterial chemotaxis, retrieving chemotactic cells off-chip based on their dynamic responses remains limited. Here, we present simple three-dimensional microfluidic platform capable programmable delivery solutions, maintaining static, stable gradients for over 20 hours, followed by active sorting retrieval bacteria phenotypes. Using this platform, revealed the swimming features individual

Язык: Английский

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Tuning dCas9's ability to block transcription enables robust, noiseless knockdown of bacterial genes

Molecular Systems Biology, Год журнала: 2018, Номер 14(3)

Опубликована: Март 1, 2018

Article8 March 2018Open Access Source DataTransparent process Tuning dCas9's ability to block transcription enables robust, noiseless knockdown of bacterial genes Antoine Vigouroux Synthetic Biology Laboratory, Institut Pasteur, Paris, France Microbial Morphogenesis and Growth Search for more papers by this author Enno Oldewurtel orcid.org/0000-0002-2813-0259 Lun Cui orcid.org/0000-0001-5907-0538 David Bikard Corresponding Author [email protected] orcid.org/0000-0002-5729-1211 Sven van Teeffelen orcid.org/0000-0002-0877-1294 Information Vigouroux1,2, Oldewurtel2, Cui1, *,1 *,2 1Synthetic 2Microbial *Corresponding author. Tel: +33 1 45 61 39 24; E-mail: 68 80 16; Molecular Systems (2018)14:e7899https://doi.org/10.15252/msb.20177899 PDFDownload PDF article text main figures. Peer ReviewDownload a summary the editorial decision including letters, reviewer comments responses feedback. ToolsAdd favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinked InMendeleyWechatReddit Figures & Info Abstract Over past few years, tools that make use Cas9 nuclease have led many breakthroughs, in control gene expression. The catalytically dead variant known as dCas9 can be guided small RNAs target genes, strategy also CRISPRi. Here, we reveal level complementarity between guide RNA controls rate at which polymerase “kicks out” from completes transcription. We mechanism precisely robustly reduce expression defined relative amounts. Alternatively, tuning repression changing concentration is noisy promoter-strength dependent. demonstrate broad applicability method study genetic regulation cellular physiology. First, characterize feedback strength model auto-repressor. Second, impact amount variations cell-wall synthesizing enzymes on cell morphology. Finally, multiplex system obtain any combination fractional two genes. Synopsis When encounters inactivated nuclease, it has certain probability going through depending sequence. This property exploited multiple their native locus. For high enough concentration, locus saturated only depends RNAP passage probability. Imperfect allows fine-tuning consequently levels. In saturating conditions, does not produce additional noise applied measure response circuit, analyze how synthesis affect shape, tune levels independently. Introduction A powerful way investigate bacteria vary cell. To end, are typically placed under inducible promoters. While easy implement, approach disadvantages: lie outside dynamic range promoter. promoters increase comparison with (Elowitz et al, 2002). And third, orthogonal systems exist, thus making multiplexing difficult. Recently, different strategies been devised knock down amounts levels: Specifically, antisense manner (Brophy Voigt, 2016). works well moderate promoter strength, becomes less efficient stronger As an alternative strategy, knocked varying degrees using CRISPR technology (Bikard 2013; Qi 2013). catalytic mutant form RNA-guided Streptococcus pyogenes (dCas9) easily programmed bind position interest chromosome, requirement “NGG” protospacer adjacent motif (PAM). unable cleave DNA, but still binds DNA strongly. If chosen downstream promoter, serves roadblock blocks elongation. single-cell level, interesting implications immune system. then develop precise noise-preserving independent strength. Target search begins probing presence PAM followed melting complementarity-dependent strand invasion (Sternberg 2014; Szczelkun 2014). PAM-proximal region seed sequence important binding, several mismatches PAM-distal tolerated demonstrated binding assays (Kuscu Wu 2014) monitoring target-gene Eschericha coli degree controlled quantitatively ways: first, impacts DNA. recently Bacillus subtilis where was xylose-inducible (Peters 2016), E. strain modified enable tunable PBAD (Li 2016); second, introducing perfectly matched leads very strong repression, decreasing progressively reduces compare these characterizing properties dCas9-mediated level. us propose novel physical repression. It previously assumed decreased would decrease virtue reduced occupancy (Farasat Salis, mechanism: inside open reading frame (ORF), determines (RNAP) kicks out during attempt, while spontaneous unbinding negligibly small. saturate target, alone desirable properties: add extrinsic On contrary, inherently target. complementarity-based fluorescent-protein reporters inserted upstream its reporter fusions rather than direct targeting yields predictable fold characterized provides monitor single cells. versatility our examples: accurate quantify auto-repressor measuring much actual differs rate. take advantage steady-state growth operon coding essential “rod” complex, PBP2 RodA. multiplexed Results Varying RNA-target controlling without addition CRISPR-dCas9 modulates integrated cassettes constitutively expressed reporters, sfgfp superfolder green fluorescent protein (GFP) mCherry red (RFP) chromosomal loci MG1655. repress either knock-down, dcas9 S. Ptet anhydrotetracycline (aTc) (Qi GFP- RFP-coding ORFs array necessary tracrRNA, complex together (Hsu Inducing setup did (Appendix Fig S1). measured stability over time saw 5 days culture. Once stopped induction all 40 clones tested recovered stable, show toxicity. system, tuned modulating aTc concentrations or spacer numbers 5′ side spacer. employed GFP high-throughput microscopy (Fig 1A B). expected, average increasing complementarity. However, distributions differed significantly modes modulation 1C D). large cell-to-cell fluctuations intermediate regime, strongly 1D Appendix S2). induced, non-repressed constitutive were recovered. expression, presumably site elaborated below. inducing constant 100 ng/ml maintained (standard deviation mean) almost plateau value about 0.3 (corresponding 30%) similar measurements made others wild-type (Taniguchi 2010). Complementarity-based qualitatively transcriptional repressors. example, Lac repressor part targets fivefold compared unrepressed case (see S3), agreement previous Accordingly, observed if modulated inducer concentration. proposed here precision Figure 1. modulate generating A, B. Average obtained (A) (B) inducer. Relative given relatively non-targeting Individual points represent replicates. Horizontal bars median three C, D. Distribution each experiment panels (A Curves same color replicates condition. Mechanistic dCas9-targeted product probabilities: P(stop) blocking upon collision occupying (termed occupancy). determined kon, [dCas9], kout. kout, turn, sum transcription-independent kick-out due 4 details). F. schematically illustrate behavior (left) (right), respectively. data available online figure. Data [msb177899-sup-0002-SDataFig1.zip] Download figure PowerPoint transcribe dCas9-bound lack suggested might test hypothesis, fraction active complexes roughly factor decoy 2A). population-averaged flow cytometry. Indeed, found absence both low 2B), confirming hypothesis 20 11 bp. remained true even spacers array, regardless S4). effectiveness confirmed gradually lowering until transition no happened higher decoys one S4B), complex. cases, induction, residual reached around 3%, corresponding concentration-independent regime. note following population averages performed cytometry generally noisier results presented 2. mismatched depend Left: Schematic assay used dependence R20 RFP perfect match. R11 bp C Introducing acts halves Right: Northern blot measurement processed R20, reflecting carrying moment measurement. Error standard deviations biological a.u.: arbitrary units. Flow levels, point representing replicate. values normalized respect (C-C). Expression differ (C-R20 vs. R20-R20, P-value: 0.68), nor when order reversed R20-C, 0.21), (C-R11 R11-R11, 0.53). P-values come two-sided Student's t-test natural logarithms mean (significance threshold: 0.017 after Bonferroni correction). 2 [msb177899-sup-0003-SDataFig2.zip] Previously, thought solely is, rates unbinding. According simple view, should lead equilibrium occupancy, fully occupied. view clear contradiction independence 2B). suggests dCas9, bound times, must responsible reconcile robustness hypothesize possible suggest ≤ 1E). = 1, efficiently every collide. At opposite extreme, 0, never 1F). mechanism, γ0 P(bound) Therefore, close saturated. longer explaining Interestingly, moved ORF region, increased S5). finding pass occupied thanks processive activity, cannot relies diffusion. know whether influence definition, Repression measurably affected strengths, verify prediction, put strengths (P127 PPhlf) blocked four number mismatches. PPhlF times P127 3A), regard promoter's initial identical 3B). 12 weaker PLac mM IPTG S6). These observations confirm conditions 3. conditionsRelative repressed set (A, B) non-saturating (C) concentrations. Raw P127, C. Experimental predicted (using lower aTc). PPhlf up six RNA, quantitative Appendix). bars: error computational prediction. 3 [msb177899-sup-0004-SDataFig3.zip] supporting “kick-out” ejection successful wondered ejected events. displacements they could RNAP, kon[dCas9] kout combined RNAP-induced ejections, possibly replication-fork-based (Jones 2017; see therefore P(bound), which, fold. observation agrees full (14 bp) complementarity, respectively 3C S7A). predicts dominated events, rare (4; S7B). compatible leaves spontaneously gets kicked replication. prediction consistent long half-life reported vivo 2017) vitro expected valid 14 bp, 1A) remains become equally collision-based ejections below some Yet, applications below, rebinding paragraph). proportional rate, principle events reads template increases temperature (Wiktor 2016) 42°C, suggesting temperature. bears possibility robust dCas9-copy temperature, condition saturation fulfilled. robustness, temperatures ranging 30 42°C. decayed continuously 4), displaying sharp 37 Regardless S8). From model, conclude being RNAP. indicates work independently tested. 4. efficiency temperaturesRelative temperatures. [msb177899-sup-0005-SDataFig4.zip] insertions contexts Precision, versatile strategy. context, insert translational gene. provide convenient CRISPR-based perform inspired allelic exchange (Pósfai 1999) Text S9). library plasmids introduced desired sequences. taking established above. Furthermore, revealing variations. addgene (https://www.addgene.org/depositor-collections/bikard-crispr-repression/). following, physiology: effect morphology growth. uncover circuits, chose described PhlF auto-repres

Язык: Английский

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Taking chances and making mistakes: non-genetic phenotypic heterogeneity and its consequences for surviving in dynamic environments

Journal of The Royal Society Interface, Год журнала: 2017, Номер 14(132), С. 20170141 - 20170141

Опубликована: Июль 1, 2017

Natural selection has shaped the strategies for survival and growth of microorganisms. The success microorganisms depends not only on slow evolutionary tuning but also ability to adapt unpredictable changes in their environment. In principle, adaptive range from purely deterministic mechanisms those that exploit randomness intrinsic many cellular molecular processes. Depending environment selective pressures, particular can lie somewhere along this continuum. recent years, non-genetic cell-to-cell differences have received a lot attention, least because potential impact microbial populations survive dynamic environments. Using several examples, we describe origins spontaneous induced phenotypic adaptation. We identify some commonalities these examples consider role chance constraints

Язык: Английский

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Spatial self-organization resolves conflicts between individuality and collective migration

Nature Communications, Год журнала: 2018, Номер 9(1)

Опубликована: Май 30, 2018

Abstract Collective behavior can spontaneously emerge when individuals follow common rules of interaction. However, the each individual differs due to existing genetic and non-genetic variation within population. It remains unclear how this individuality is managed achieve collective behavior. We quantify in bands clonal Escherichia coli cells that migrate collectively along a channel by following self-generated gradient attractant. discover despite substantial differences chemotactic abilities, are able as coherent group sorting themselves moving band. This mechanism ensures between abilities compensated local steepness traveling must navigate, determines minimum performance required travel with By resolving conflicts migration, enables populations maintain advantageous diversity while on move.

Язык: Английский

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Wide lag time distributions break a trade-off between reproduction and survival in bacteria

Proceedings of the National Academy of Sciences, Год журнала: 2020, Номер 117(31), С. 18729 - 18736

Опубликована: Июль 15, 2020

Significance The biology of many microorganisms has been adapted to a feast-and-famine lifestyle. Thus, understanding population dynamics during transitions from starvation resource abundance is important for fundamental and applied reasons. Here, we study starved populations bacteria encountering new resources ask how the behavior single cells gives rise emergent population-level traits. We find that growth survival are dominated by phenotypic minorities: small subpopulations with extreme lag times. As consequence, can break life history trade-off between evolving variation in time. By showing why sustain long times our findings explain prevalence antibiotic tolerance lag.

Язык: Английский

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Emergent properties of bacterial chemotaxis pathway

Current Opinion in Microbiology, Год журнала: 2017, Номер 39, С. 24 - 33

Опубликована: Авг. 17, 2017

Язык: Английский

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Bacterial chemotaxis in a microfluidic T-maze reveals strong phenotypic heterogeneity in chemotactic sensitivity

Nature Communications, Год журнала: 2019, Номер 10(1)

Опубликована: Апрель 23, 2019

Many microorganisms have evolved chemotactic strategies to exploit the microscale heterogeneity that frequently characterizes microbial habitats. Chemotaxis has been primarily studied as an average characteristic of a population, with little regard for variability among individuals. Here, we adopt classic tool from animal ecology - T-maze and implement it at by using microfluidics expose bacteria sequence decisions, each consisting migration up or down chemical gradient. Single-cell observations clonal Escherichia coli in maze, coupled mathematical model, reveal strong sensitivity coefficient exists even within populations bacteria. A comparison different potential sources reveals originates coefficient, arising distribution pathway gains. This may functional role, example context migratory bet-hedging strategies.

Язык: Английский

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